I fear we have a bug there. Open the customfield.php in sublayout ( /components/com_virtuemart/sublayouts) and replace the foreach ( foreach( (array)$product->customfields as $prodcustom){ ) around line658 with this

//We just add the customfields to be shown in the cart to the variantmodsif(is_object($prodcustom)){if($prodcustom->is_cart_attribute or $prodcustom->is_input){if(!isset($variantmods[$prodcustom->virtuemart_custom_id])){$variantmods[$prodcustom->virtuemart_custom_id][$prodcustom->virtuemart_customfield_id] = true;}}$productCustoms[$prodcustom->virtuemart_customfield_id] = $prodcustom;}}

I fear we have a bug there. Open the customfield.php in sublayout ( /components/com_virtuemart/sublayouts) and replace the foreach ( foreach( (array)$product->customfields as $prodcustom){ ) around line658 with this

//We just add the customfields to be shown in the cart to the variantmodsif(is_object($prodcustom)){if($prodcustom->is_cart_attribute or $prodcustom->is_input){if(!isset($variantmods[$prodcustom->virtuemart_custom_id])){$variantmods[$prodcustom->virtuemart_custom_id][$prodcustom->virtuemart_customfield_id] = true;}}$productCustoms[$prodcustom->virtuemart_customfield_id] = $prodcustom;}}

Thank you Milbo - I can verify this works following the recent upgrade when the Custom fields disappeared.